Popper made the mistake of regarding Freud as a scientist whereas in reality Freud merely made unfounded assertions (basically he just recreated the Christian tripartite deity in his own baroque mythology). Secondly, while real science very often does not conform to the naive notion of hypothesis-theory-observation/falsification it does however rest entirely on empiricism. Regardless of the state of incompleteness of any modern theories, the criterion for acceptance is their predictive strength. Theories lacking in measurable predictive strength are held at best tentatively and we wait until evidence in support or in contradiction of such theories is achieved.
Ironically, as a philosopher of science Popper failed in many ways to understand the essence of how science actually works, and he certainly failed to achieve an adequate theoretical description of it. Perhaps this was inevitable, as it can be argued that “philosophy was what people had before we developed science.”